Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 20 00:28:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nww_12636/07_2023/7nww_12636_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nww_12636/07_2023/7nww_12636.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nww_12636/07_2023/7nww_12636_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nww_12636/07_2023/7nww_12636_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nww_12636/07_2023/7nww_12636_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nww_12636/07_2023/7nww_12636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nww_12636/07_2023/7nww_12636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nww_12636/07_2023/7nww_12636_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nww_12636/07_2023/7nww_12636_updated.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4651 5.49 5 Mg 413 5.21 5 S 150 5.16 5 C 72657 2.51 5 N 26976 2.21 5 O 40300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H ARG 68": "NH1" <-> "NH2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I ARG 37": "NH1" <-> "NH2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I ARG 120": "NH1" <-> "NH2" Residue "J ARG 17": "NH1" <-> "NH2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K ARG 33": "NH1" <-> "NH2" Residue "K ARG 41": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K GLU 51": "OE1" <-> "OE2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ARG 78": "NH1" <-> "NH2" Residue "K ARG 123": "NH1" <-> "NH2" Residue "K ARG 126": "NH1" <-> "NH2" Residue "L ARG 10": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L GLU 75": "OE1" <-> "OE2" Residue "L ARG 114": "NH1" <-> "NH2" Residue "M ARG 8": "NH1" <-> "NH2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "M ARG 17": "NH1" <-> "NH2" Residue "M ARG 22": "NH1" <-> "NH2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M ARG 69": "NH1" <-> "NH2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N ARG 25": "NH1" <-> "NH2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N ARG 94": "NH1" <-> "NH2" Residue "N ARG 102": "NH1" <-> "NH2" Residue "N ARG 111": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O ARG 62": "NH1" <-> "NH2" Residue "O ARG 89": "NH1" <-> "NH2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "O GLU 102": "OE1" <-> "OE2" Residue "O ARG 109": "NH1" <-> "NH2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "P ARG 13": "NH1" <-> "NH2" Residue "P ARG 33": "NH1" <-> "NH2" Residue "P ARG 48": "NH1" <-> "NH2" Residue "P ARG 70": "NH1" <-> "NH2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 68": "NH1" <-> "NH2" Residue "Q ARG 78": "NH1" <-> "NH2" Residue "Q ARG 79": "NH1" <-> "NH2" Residue "Q ARG 84": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R ARG 92": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "S ARG 3": "NH1" <-> "NH2" Residue "S ARG 6": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T ARG 82": "NH1" <-> "NH2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ARG 94": "NH1" <-> "NH2" Residue "U ARG 19": "NH1" <-> "NH2" Residue "W ARG 3": "NH1" <-> "NH2" Residue "W ARG 18": "NH1" <-> "NH2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "W ARG 45": "NH1" <-> "NH2" Residue "W ARG 50": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "X ARG 29": "NH1" <-> "NH2" Residue "X ARG 47": "NH1" <-> "NH2" Residue "X ARG 52": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 30": "NH1" <-> "NH2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Z ARG 56": "NH1" <-> "NH2" Residue "Z ARG 63": "NH1" <-> "NH2" Residue "a ARG 10": "NH1" <-> "NH2" Residue "a ARG 16": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b ARG 44": "NH1" <-> "NH2" Residue "c ARG 3": "NH1" <-> "NH2" Residue "c ARG 14": "NH1" <-> "NH2" Residue "c ARG 19": "NH1" <-> "NH2" Residue "c ARG 21": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 41": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 42": "NH1" <-> "NH2" Residue "e ARG 24": "NH1" <-> "NH2" Residue "f ARG 63": "NH1" <-> "NH2" Residue "f ARG 74": "NH1" <-> "NH2" Residue "f GLU 78": "OE1" <-> "OE2" Residue "f ARG 208": "NH1" <-> "NH2" Residue "f ARG 225": "NH1" <-> "NH2" Residue "g ARG 54": "NH1" <-> "NH2" Residue "g ARG 72": "NH1" <-> "NH2" Residue "g ARG 88": "NH1" <-> "NH2" Residue "g ARG 127": "NH1" <-> "NH2" Residue "g ARG 131": "NH1" <-> "NH2" Residue "g ARG 132": "NH1" <-> "NH2" Residue "g ARG 164": "NH1" <-> "NH2" Residue "h ARG 73": "NH1" <-> "NH2" Residue "h ARG 81": "NH1" <-> "NH2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i ARG 68": "NH1" <-> "NH2" Residue "i ARG 69": "NH1" <-> "NH2" Residue "i ARG 93": "NH1" <-> "NH2" Residue "i GLU 116": "OE1" <-> "OE2" Residue "i ARG 157": "NH1" <-> "NH2" Residue "j PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 79": "NH1" <-> "NH2" Residue "k ARG 4": "NH1" <-> "NH2" Residue "k ARG 53": "NH1" <-> "NH2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "k GLU 90": "OE1" <-> "OE2" Residue "k ARG 92": "NH1" <-> "NH2" Residue "l GLU 91": "OE1" <-> "OE2" Residue "m ARG 11": "NH1" <-> "NH2" Residue "m ARG 41": "NH1" <-> "NH2" Residue "m ARG 130": "NH1" <-> "NH2" Residue "n ARG 5": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "n ARG 89": "NH1" <-> "NH2" Residue "o ARG 37": "NH1" <-> "NH2" Residue "o ARG 69": "NH1" <-> "NH2" Residue "o ARG 93": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 14": "NH1" <-> "NH2" Residue "p ARG 50": "NH1" <-> "NH2" Residue "p ARG 83": "NH1" <-> "NH2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q GLU 50": "OE1" <-> "OE2" Residue "q ARG 70": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "q ARG 109": "NH1" <-> "NH2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r ARG 63": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "r ARG 69": "NH1" <-> "NH2" Residue "r ARG 85": "NH1" <-> "NH2" Residue "s ARG 72": "NH1" <-> "NH2" Residue "s ARG 89": "NH1" <-> "NH2" Residue "t ARG 28": "NH1" <-> "NH2" Residue "t ARG 51": "NH1" <-> "NH2" Residue "u ARG 11": "NH1" <-> "NH2" Residue "u ARG 27": "NH1" <-> "NH2" Residue "u ARG 65": "NH1" <-> "NH2" Residue "u ARG 77": "NH1" <-> "NH2" Residue "v ARG 61": "NH1" <-> "NH2" Residue "w ARG 32": "NH1" <-> "NH2" Residue "x ARG 60": "NH1" <-> "NH2" Residue "x ARG 74": "NH1" <-> "NH2" Residue "y ARG 33": "NH1" <-> "NH2" Residue "y GLU 44": "OE1" <-> "OE2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "y ARG 55": "NH1" <-> "NH2" Residue "y ARG 62": "NH1" <-> "NH2" Residue "y ARG 67": "NH1" <-> "NH2" Residue "y ARG 69": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 145149 Number of models: 1 Model: "" Number of chains: 67 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 289, 'rna2p_pyr': 166, 'rna3p': 16, 'rna3p_pur': 1378, 'rna3p_pyr': 1048} Link IDs: {'rna2p': 460, 'rna3p': 2442} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 117, 'rna2p_pyr': 89, 'rna3p': 10, 'rna3p_pur': 752, 'rna3p_pyr': 564} Link IDs: {'rna2p': 206, 'rna3p': 1327} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "4" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna3p': 5} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "I" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "K" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "L" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "M" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "O" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "P" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "Q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "S" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "T" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "U" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "V" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 601 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "W" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Y" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "Z" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "a" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "b" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "c" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "d" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "e" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "f" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "g" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "h" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "i" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "j" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "k" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "l" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "m" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "n" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "o" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "p" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "r" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "s" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "t" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "u" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "v" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "w" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "x" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "y" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "z" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1891 Inner-chain residues flagged as termini: ['pdbres=" U z 8 "', 'pdbres=" G z 9 "', 'pdbres=" U z 20 "', 'pdbres=" U z 67 "'] Classifications: {'RNA': 88} Modifications used: {'p5*END': 4, 'rna2p': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p': 1, 'rna3p_pur': 40, 'rna3p_pyr': 33} Link IDs: {'rna2p': 13, 'rna3p': 74} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 205 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 278 Unusual residues: {' MG': 278} Classifications: {'undetermined': 278} Link IDs: {None: 277} Chain: "2" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Unusual residues: {' MG': 119} Classifications: {'undetermined': 119} Link IDs: {None: 118} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0GBZ SG CYS Z 16 65.955 60.282 105.737 1.00 98.48 S ATOM A0GCB SG CYS Z 18 64.040 58.774 102.500 1.00 99.69 S ATOM A0GG9 SG CYS Z 37 66.673 59.020 101.796 1.00 97.54 S ATOM A0GGU SG CYS Z 40 65.282 62.092 102.396 1.00 98.28 S ATOM A0I1V SG CYS e 11 144.168 116.647 47.922 1.00 71.97 S ATOM A0I2K SG CYS e 14 146.772 115.024 49.360 1.00 69.39 S ATOM A0I5F SG CYS e 27 146.602 118.948 47.975 1.00 69.95 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13143 " occ=0.50 Time building chain proxies: 49.59, per 1000 atoms: 0.34 Number of scatterers: 145149 At special positions: 0 Unit cell: (277.13, 267.5, 228.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 150 16.00 P 4651 15.00 Mg 413 11.99 O 40300 8.00 N 26976 7.00 C 72657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 59.35 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Z 101 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 37 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 40 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 16 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 18 " pdb=" ZN e 101 " pdb="ZN ZN e 101 " - pdb=" ND1 HIS e 33 " pdb="ZN ZN e 101 " - pdb=" SG CYS e 27 " pdb="ZN ZN e 101 " - pdb=" SG CYS e 11 " pdb="ZN ZN e 101 " - pdb=" SG CYS e 14 " Number of angles added : 9 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10532 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 177 helices and 74 sheets defined 39.1% alpha, 20.2% beta 1573 base pairs and 2645 stacking pairs defined. Time for finding SS restraints: 58.25 Creating SS restraints... Processing helix chain 'C' and resid 10 through 16 removed outlier: 7.544A pdb=" N HIS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.812A pdb=" N LEU C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.060A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.453A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 4.093A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N PHE C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'D' and resid 56 through 61 removed outlier: 5.837A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.660A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.128A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.682A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 6.598A pdb=" N THR E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.450A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 removed outlier: 6.335A pdb=" N ASP E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 2 through 21 removed outlier: 5.127A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.043A pdb=" N ASP F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 42 through 47' Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.558A pdb=" N ALA F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 5.402A pdb=" N VAL F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 142 through 147 removed outlier: 3.557A pdb=" N VAL F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ASP F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 147' Processing helix chain 'F' and resid 162 through 174 removed outlier: 4.404A pdb=" N GLY F 166 " --> pdb=" O SER F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.706A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Proline residue: F 139 - end of helix Processing helix chain 'G' and resid 2 through 8 removed outlier: 3.834A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 60 through 81 removed outlier: 3.593A pdb=" N GLN G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.652A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 50 removed outlier: 4.300A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 74 removed outlier: 4.626A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA H 74 " --> pdb=" O GLU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'I' and resid 24 through 38 removed outlier: 4.103A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 96 Processing helix chain 'I' and resid 97 through 110 removed outlier: 4.476A pdb=" N ILE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 123 removed outlier: 3.862A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LYS I 123 " --> pdb=" O PHE I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 removed outlier: 4.471A pdb=" N LYS I 72 " --> pdb=" O ASN I 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 67 through 72' Processing helix chain 'J' and resid 112 through 119 Processing helix chain 'K' and resid 37 through 42 removed outlier: 4.180A pdb=" N ARG K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N SER K 42 " --> pdb=" O GLN K 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 37 through 42' Processing helix chain 'K' and resid 56 through 62 Proline residue: K 62 - end of helix Processing helix chain 'K' and resid 68 through 75 removed outlier: 3.873A pdb=" N ALA K 72 " --> pdb=" O SER K 68 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 85 removed outlier: 4.076A pdb=" N LEU K 82 " --> pdb=" O ARG K 78 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA K 83 " --> pdb=" O LEU K 79 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 78 through 85' Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 128 through 139 Processing helix chain 'L' and resid 42 through 58 Processing helix chain 'L' and resid 109 through 125 removed outlier: 3.916A pdb=" N LYS L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Proline residue: L 125 - end of helix Processing helix chain 'M' and resid 13 through 32 Processing helix chain 'M' and resid 38 through 57 removed outlier: 3.593A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.589A pdb=" N THR M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 3.626A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) Proline residue: M 85 - end of helix Processing helix chain 'N' and resid 2 through 22 removed outlier: 4.530A pdb=" N ARG N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ALA N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG N 16 " --> pdb=" O THR N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 63 removed outlier: 4.920A pdb=" N GLN N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU N 62 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 86 Processing helix chain 'N' and resid 101 through 114 Processing helix chain 'O' and resid 2 through 13 removed outlier: 3.583A pdb=" N GLU O 11 " --> pdb=" O GLN O 7 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN O 12 " --> pdb=" O LEU O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 104 removed outlier: 3.758A pdb=" N ARG O 103 " --> pdb=" O TYR O 99 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N THR O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 99 through 104' Processing helix chain 'P' and resid 6 through 22 removed outlier: 3.760A pdb=" N ILE P 17 " --> pdb=" O ARG P 13 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.818A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.907A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG P 58 " --> pdb=" O LYS P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 87 removed outlier: 3.594A pdb=" N ASN P 81 " --> pdb=" O SER P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 102 Processing helix chain 'P' and resid 103 through 118 Processing helix chain 'R' and resid 13 through 25 removed outlier: 3.740A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG R 25 " --> pdb=" O ALA R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 41 through 61 removed outlier: 3.775A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 3.673A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LYS R 70 " --> pdb=" O ILE R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 70' Processing helix chain 'S' and resid 3 through 11 removed outlier: 4.340A pdb=" N LEU S 11 " --> pdb=" O LEU S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 27 Processing helix chain 'S' and resid 39 through 50 Processing helix chain 'T' and resid 66 through 71 removed outlier: 3.892A pdb=" N VAL T 70 " --> pdb=" O GLN T 66 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 66 through 71' Processing helix chain 'U' and resid 13 through 24 Processing helix chain 'U' and resid 43 through 53 removed outlier: 3.684A pdb=" N VAL U 47 " --> pdb=" O ASP U 43 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA U 52 " --> pdb=" O MET U 48 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS U 53 " --> pdb=" O ASN U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 59 Processing helix chain 'W' and resid 52 through 63 Processing helix chain 'W' and resid 64 through 75 Processing helix chain 'X' and resid 2 through 10 removed outlier: 3.690A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS X 9 " --> pdb=" O GLU X 5 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER X 10 " --> pdb=" O LEU X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 35 removed outlier: 4.150A pdb=" N GLY X 35 " --> pdb=" O GLN X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 62 removed outlier: 4.255A pdb=" N LYS X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLY X 62 " --> pdb=" O ASN X 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 28 Processing helix chain 'Y' and resid 41 through 52 Processing helix chain 'Z' and resid 44 through 51 removed outlier: 5.427A pdb=" N GLN Z 48 " --> pdb=" O PHE Z 44 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL Z 51 " --> pdb=" O LYS Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 65 removed outlier: 4.145A pdb=" N PHE Z 64 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASN Z 65 " --> pdb=" O ASN Z 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 21 removed outlier: 4.763A pdb=" N HIS a 19 " --> pdb=" O MET a 15 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASP a 20 " --> pdb=" O ARG a 16 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA a 21 " --> pdb=" O ARG a 17 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 31 Proline residue: b 31 - end of helix Processing helix chain 'c' and resid 8 through 16 Processing helix chain 'c' and resid 17 through 25 removed outlier: 4.311A pdb=" N THR c 24 " --> pdb=" O ALA c 20 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LYS c 25 " --> pdb=" O ARG c 21 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 38 Processing helix chain 'd' and resid 7 through 14 Processing helix chain 'd' and resid 32 through 37 removed outlier: 4.603A pdb=" N LYS d 36 " --> pdb=" O ILE d 32 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA d 37 " --> pdb=" O LEU d 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 32 through 37' Processing helix chain 'd' and resid 38 through 46 Proline residue: d 46 - end of helix Processing helix chain 'd' and resid 51 through 63 removed outlier: 4.689A pdb=" N GLY d 56 " --> pdb=" O LYS d 52 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU d 57 " --> pdb=" O GLY d 53 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL d 58 " --> pdb=" O ASP d 54 " (cutoff:3.500A) Proline residue: d 63 - end of helix Processing helix chain 'f' and resid 5 through 13 Processing helix chain 'f' and resid 27 through 32 removed outlier: 5.529A pdb=" N PHE f 32 " --> pdb=" O LYS f 28 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 64 Proline residue: f 48 - end of helix Processing helix chain 'f' and resid 73 through 88 removed outlier: 6.199A pdb=" N SER f 77 " --> pdb=" O LYS f 73 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU f 78 " --> pdb=" O ARG f 74 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ALA f 79 " --> pdb=" O ALA f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 103 through 122 removed outlier: 4.203A pdb=" N GLN f 109 " --> pdb=" O LYS f 105 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER f 110 " --> pdb=" O THR f 106 " (cutoff:3.500A) Processing helix chain 'f' and resid 130 through 148 Processing helix chain 'f' and resid 165 through 170 Processing helix chain 'f' and resid 171 through 180 Processing helix chain 'f' and resid 206 through 227 Processing helix chain 'g' and resid 6 through 12 Processing helix chain 'g' and resid 28 through 48 removed outlier: 3.627A pdb=" N ASN g 32 " --> pdb=" O GLU g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 72 through 78 removed outlier: 3.970A pdb=" N VAL g 76 " --> pdb=" O ARG g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 96 removed outlier: 3.637A pdb=" N VAL g 90 " --> pdb=" O LYS g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 108 through 113 removed outlier: 4.445A pdb=" N ASP g 112 " --> pdb=" O LYS g 108 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ALA g 113 " --> pdb=" O PRO g 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 108 through 113' Processing helix chain 'g' and resid 114 through 127 Processing helix chain 'g' and resid 129 through 145 Processing helix chain 'h' and resid 7 through 16 removed outlier: 4.110A pdb=" N LEU h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 27 through 32 Processing helix chain 'h' and resid 49 through 66 Processing helix chain 'h' and resid 68 through 83 removed outlier: 5.261A pdb=" N LYS h 83 " --> pdb=" O ALA h 79 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 97 Processing helix chain 'h' and resid 98 through 106 Processing helix chain 'h' and resid 110 through 121 Processing helix chain 'h' and resid 152 through 166 removed outlier: 3.887A pdb=" N LYS h 156 " --> pdb=" O GLN h 152 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU h 163 " --> pdb=" O LEU h 159 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN h 164 " --> pdb=" O GLU h 160 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU h 166 " --> pdb=" O ALA h 162 " (cutoff:3.500A) Processing helix chain 'h' and resid 187 through 192 removed outlier: 3.625A pdb=" N LEU h 191 " --> pdb=" O GLU h 187 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N SER h 192 " --> pdb=" O ARG h 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 187 through 192' Processing helix chain 'h' and resid 196 through 206 removed outlier: 3.916A pdb=" N ILE h 200 " --> pdb=" O ASN h 196 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS h 206 " --> pdb=" O GLU h 202 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 71 removed outlier: 3.697A pdb=" N ARG i 69 " --> pdb=" O GLU i 65 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN i 70 " --> pdb=" O LYS i 66 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N MET i 71 " --> pdb=" O ALA i 67 " (cutoff:3.500A) Processing helix chain 'i' and resid 109 through 119 removed outlier: 3.854A pdb=" N ALA i 113 " --> pdb=" O GLY i 109 " (cutoff:3.500A) Processing helix chain 'i' and resid 132 through 147 Processing helix chain 'i' and resid 149 through 158 Processing helix chain 'i' and resid 160 through 165 Processing helix chain 'j' and resid 11 through 19 removed outlier: 3.859A pdb=" N SER j 15 " --> pdb=" O HIS j 11 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLU j 16 " --> pdb=" O PRO j 12 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN j 17 " --> pdb=" O ASP j 13 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL j 18 " --> pdb=" O GLN j 14 " (cutoff:3.500A) Proline residue: j 19 - end of helix No H-bonds generated for 'chain 'j' and resid 11 through 19' Processing helix chain 'j' and resid 20 through 33 Processing helix chain 'j' and resid 67 through 81 removed outlier: 3.650A pdb=" N ILE j 71 " --> pdb=" O PRO j 67 " (cutoff:3.500A) Processing helix chain 'k' and resid 20 through 31 Processing helix chain 'k' and resid 35 through 55 removed outlier: 3.703A pdb=" N ALA k 39 " --> pdb=" O LYS k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 70 removed outlier: 3.772A pdb=" N VAL k 69 " --> pdb=" O ALA k 65 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 111 Processing helix chain 'k' and resid 115 through 130 Processing helix chain 'k' and resid 132 through 149 Processing helix chain 'l' and resid 5 through 21 Processing helix chain 'l' and resid 30 through 44 Processing helix chain 'l' and resid 112 through 120 Processing helix chain 'm' and resid 34 through 39 Processing helix chain 'm' and resid 41 through 56 removed outlier: 3.598A pdb=" N ARG m 49 " --> pdb=" O ARG m 45 " (cutoff:3.500A) Proline residue: m 51 - end of helix removed outlier: 4.227A pdb=" N ASP m 56 " --> pdb=" O LEU m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 71 through 92 Processing helix chain 'm' and resid 94 through 102 removed outlier: 4.209A pdb=" N LYS m 100 " --> pdb=" O SER m 96 " (cutoff:3.500A) Processing helix chain 'n' and resid 14 through 33 removed outlier: 3.708A pdb=" N GLU n 27 " --> pdb=" O ALA n 23 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR n 28 " --> pdb=" O GLU n 24 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA n 29 " --> pdb=" O ILE n 25 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 5.195A pdb=" N ASP n 91 " --> pdb=" O LEU n 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 46 through 51 removed outlier: 4.193A pdb=" N GLY o 51 " --> pdb=" O ALA o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 54 through 59 removed outlier: 3.930A pdb=" N SER o 58 " --> pdb=" O GLY o 54 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR o 59 " --> pdb=" O SER o 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 54 through 59' Processing helix chain 'o' and resid 60 through 75 Processing helix chain 'o' and resid 93 through 104 removed outlier: 5.270A pdb=" N ILE o 97 " --> pdb=" O ARG o 93 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 10 Processing helix chain 'p' and resid 113 through 118 removed outlier: 3.912A pdb=" N TYR p 117 " --> pdb=" O ALA p 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 22 removed outlier: 4.285A pdb=" N ILE q 22 " --> pdb=" O ALA q 18 " (cutoff:3.500A) Processing helix chain 'q' and resid 26 through 38 Processing helix chain 'q' and resid 49 through 64 removed outlier: 4.210A pdb=" N PHE q 63 " --> pdb=" O GLU q 59 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL q 64 " --> pdb=" O VAL q 60 " (cutoff:3.500A) Processing helix chain 'q' and resid 66 through 84 Processing helix chain 'q' and resid 85 through 94 Processing helix chain 'q' and resid 106 through 111 Processing helix chain 'r' and resid 3 through 21 removed outlier: 3.868A pdb=" N PHE r 21 " --> pdb=" O ALA r 17 " (cutoff:3.500A) Processing helix chain 'r' and resid 22 through 33 Processing helix chain 'r' and resid 37 through 52 Proline residue: r 52 - end of helix Processing helix chain 'r' and resid 80 through 91 Processing helix chain 's' and resid 4 through 16 Processing helix chain 's' and resid 24 through 43 removed outlier: 4.587A pdb=" N GLY s 41 " --> pdb=" O ASN s 37 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS s 42 " --> pdb=" O HIS s 38 " (cutoff:3.500A) Processing helix chain 's' and resid 49 through 74 removed outlier: 3.839A pdb=" N GLY s 55 " --> pdb=" O HIS s 51 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 86 Processing helix chain 't' and resid 53 through 64 Processing helix chain 't' and resid 68 through 82 Processing helix chain 'v' and resid 11 through 17 Processing helix chain 'v' and resid 25 through 34 removed outlier: 5.762A pdb=" N THR v 34 " --> pdb=" O LYS v 30 " (cutoff:3.500A) Processing helix chain 'v' and resid 41 through 46 removed outlier: 3.681A pdb=" N THR v 45 " --> pdb=" O PRO v 41 " (cutoff:3.500A) Processing helix chain 'v' and resid 48 through 66 removed outlier: 3.798A pdb=" N ARG v 61 " --> pdb=" O ARG v 57 " (cutoff:3.500A) Processing helix chain 'w' and resid 12 through 26 Processing helix chain 'w' and resid 70 through 76 removed outlier: 4.398A pdb=" N PHE w 74 " --> pdb=" O LYS w 70 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA w 75 " --> pdb=" O LEU w 71 " (cutoff:3.500A) Proline residue: w 76 - end of helix No H-bonds generated for 'chain 'w' and resid 70 through 76' Processing helix chain 'w' and resid 64 through 69 removed outlier: 3.586A pdb=" N VAL w 67 " --> pdb=" O ASP w 64 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY w 68 " --> pdb=" O GLU w 65 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS w 69 " --> pdb=" O MET w 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 64 through 69' Processing helix chain 'x' and resid 4 through 41 Processing helix chain 'x' and resid 44 through 65 Proline residue: x 56 - end of helix Processing helix chain 'x' and resid 68 through 87 removed outlier: 4.830A pdb=" N ALA x 87 " --> pdb=" O ILE x 83 " (cutoff:3.500A) Processing helix chain 'y' and resid 11 through 27 Processing helix chain 'y' and resid 28 through 37 removed outlier: 5.086A pdb=" N PHE y 37 " --> pdb=" O ARG y 33 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 69 removed outlier: 4.180A pdb=" N LYS y 59 " --> pdb=" O ARG y 55 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG y 67 " --> pdb=" O GLU y 63 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR y 68 " --> pdb=" O ASN y 64 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG y 69 " --> pdb=" O ALA y 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 16 removed outlier: 4.482A pdb=" N LYS B 16 " --> pdb=" O PHE B 12 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 2 through 5 Processing sheet with id= 2, first strand: chain 'C' and resid 80 through 83 removed outlier: 6.620A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.240A pdb=" N SER C 139 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 163 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.455A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.412A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 13.324A pdb=" N GLY D 198 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 11.808A pdb=" N LYS D 114 " --> pdb=" O GLY D 198 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.850A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 179 through 182 Processing sheet with id= 8, first strand: chain 'D' and resid 24 through 28 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'D' and resid 46 through 51 removed outlier: 5.725A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.145A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 1 through 6 removed outlier: 4.330A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 117 through 120 Processing sheet with id= 13, first strand: chain 'F' and resid 65 through 69 removed outlier: 4.894A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 72 through 75 removed outlier: 5.185A pdb=" N SER F 73 " --> pdb=" O ARG F 80 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG F 80 " --> pdb=" O SER F 73 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA F 75 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 16 through 19 removed outlier: 3.777A pdb=" N ASP G 16 " --> pdb=" O LYS G 27 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 17, first strand: chain 'G' and resid 82 through 89 removed outlier: 5.840A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 19, first strand: chain 'H' and resid 17 through 20 removed outlier: 4.476A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 76 through 83 removed outlier: 4.938A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 142 " --> pdb=" O VAL H 130 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL H 130 " --> pdb=" O VAL H 142 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL H 144 " --> pdb=" O HIS H 128 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS H 128 " --> pdb=" O VAL H 144 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 52 through 57 removed outlier: 4.730A pdb=" N ASP I 19 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 74 through 78 removed outlier: 7.133A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.095A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 38 through 41 Processing sheet with id= 25, first strand: chain 'J' and resid 68 through 71 removed outlier: 3.786A pdb=" N SER J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'K' and resid 119 through 123 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'L' and resid 37 through 40 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'L' and resid 62 through 65 removed outlier: 3.603A pdb=" N TYR L 103 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU L 33 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS L 100 " --> pdb=" O ALA L 35 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'L' and resid 73 through 76 removed outlier: 6.869A pdb=" N ILE L 73 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'L' and resid 30 through 36 removed outlier: 8.209A pdb=" N SER L 30 " --> pdb=" O LYS L 133 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS L 127 " --> pdb=" O VAL L 36 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.162A pdb=" N ARG M 103 " --> pdb=" O ASN M 107 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY M 101 " --> pdb=" O PRO M 109 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA M 111 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS M 99 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE M 113 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE M 97 " --> pdb=" O ILE M 113 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU M 115 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR M 95 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'N' and resid 49 through 52 removed outlier: 3.910A pdb=" N VAL N 49 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'O' and resid 38 through 45 removed outlier: 6.722A pdb=" N THR O 25 " --> pdb=" O LYS O 87 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'O' and resid 49 through 53 removed outlier: 3.756A pdb=" N ALA O 49 " --> pdb=" O THR O 60 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG O 53 " --> pdb=" O HIS O 56 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N SER O 57 " --> pdb=" O THR O 76 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Q' and resid 11 through 15 removed outlier: 3.654A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN Q 43 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU Q 46 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Q' and resid 18 through 23 removed outlier: 4.673A pdb=" N GLN Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP Q 95 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 38, first strand: chain 'Q' and resid 65 through 77 removed outlier: 4.998A pdb=" N GLN Q 91 " --> pdb=" O GLY Q 69 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS Q 71 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N HIS Q 89 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS Q 73 " --> pdb=" O GLN Q 87 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN Q 87 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL Q 75 " --> pdb=" O LYS Q 85 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS Q 85 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE Q 77 " --> pdb=" O TYR Q 83 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N TYR Q 83 " --> pdb=" O PHE Q 77 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 40, first strand: chain 'S' and resid 12 through 15 removed outlier: 5.158A pdb=" N VAL S 31 " --> pdb=" O HIS S 15 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ASN S 28 " --> pdb=" O LEU S 87 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS S 81 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS S 66 " --> pdb=" O ARG S 77 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ASP S 79 " --> pdb=" O LYS S 64 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS S 64 " --> pdb=" O ASP S 79 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS S 81 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL S 62 " --> pdb=" O LYS S 81 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA S 83 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR S 60 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL S 85 " --> pdb=" O VAL S 58 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL S 58 " --> pdb=" O VAL S 85 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'T' and resid 40 through 46 removed outlier: 4.959A pdb=" N ASN T 40 " --> pdb=" O ALA T 63 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= 43, first strand: chain 'U' and resid 69 through 72 removed outlier: 3.653A pdb=" N ILE U 89 " --> pdb=" O PRO U 27 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 51 through 54 removed outlier: 4.404A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.573A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 35 through 41 Processing sheet with id= 47, first strand: chain 'Y' and resid 33 through 39 removed outlier: 4.007A pdb=" N HIS Y 34 " --> pdb=" O GLN Y 9 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N MET Y 54 " --> pdb=" O THR Y 10 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'Z' and resid 20 through 25 removed outlier: 4.135A pdb=" N ASN Z 20 " --> pdb=" O CYS Z 16 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'a' and resid 29 through 32 removed outlier: 4.396A pdb=" N GLU a 36 " --> pdb=" O ASP a 31 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'b' and resid 19 through 25 removed outlier: 6.026A pdb=" N HIS b 19 " --> pdb=" O SER b 13 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE b 48 " --> pdb=" O SER b 14 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU b 34 " --> pdb=" O GLU b 51 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'd' and resid 22 through 25 removed outlier: 5.576A pdb=" N PHE d 22 " --> pdb=" O VAL d 50 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'f' and resid 15 through 18 removed outlier: 5.117A pdb=" N HIS f 15 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY f 17 " --> pdb=" O HIS f 39 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N HIS f 39 " --> pdb=" O GLY f 17 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'f' and resid 89 through 93 Processing sheet with id= 54, first strand: chain 'g' and resid 53 through 59 removed outlier: 3.586A pdb=" N ARG g 54 " --> pdb=" O HIS g 69 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'g' and resid 164 through 169 removed outlier: 6.031A pdb=" N ARG g 164 " --> pdb=" O GLY g 155 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP g 181 " --> pdb=" O LYS g 204 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'h' and resid 141 through 145 removed outlier: 6.410A pdb=" N MET h 178 " --> pdb=" O ILE h 145 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'i' and resid 11 through 16 removed outlier: 7.065A pdb=" N LEU i 36 " --> pdb=" O ILE i 16 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'i' and resid 84 through 88 removed outlier: 3.637A pdb=" N ALA i 99 " --> pdb=" O ASN i 122 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN i 122 " --> pdb=" O ALA i 99 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'i' and resid 33 through 41 removed outlier: 6.700A pdb=" N ARG i 45 " --> pdb=" O ASP i 41 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'j' and resid 38 through 42 removed outlier: 3.988A pdb=" N ARG j 38 " --> pdb=" O ASN j 63 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR j 59 " --> pdb=" O TRP j 42 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS j 3 " --> pdb=" O THR j 92 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 43 through 47 removed outlier: 3.722A pdb=" N GLY j 43 " --> pdb=" O TYR j 59 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N HIS j 55 " --> pdb=" O LEU j 47 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'k' and resid 72 through 79 removed outlier: 5.907A pdb=" N THR k 72 " --> pdb=" O VAL k 91 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TYR k 85 " --> pdb=" O ARG k 78 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'l' and resid 23 through 29 removed outlier: 6.818A pdb=" N ALA l 23 " --> pdb=" O LEU l 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP l 48 " --> pdb=" O THR l 62 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'l' and resid 74 through 77 removed outlier: 3.704A pdb=" N CYS l 127 " --> pdb=" O VAL l 103 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL l 103 " --> pdb=" O ILE l 126 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'm' and resid 5 through 11 Processing sheet with id= 66, first strand: chain 'n' and resid 35 through 38 removed outlier: 7.595A pdb=" N GLN n 35 " --> pdb=" O VAL n 77 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP n 75 " --> pdb=" O ARG n 37 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG n 5 " --> pdb=" O GLY n 103 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'n' and resid 42 through 52 removed outlier: 4.722A pdb=" N LEU n 71 " --> pdb=" O PRO n 43 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'o' and resid 30 through 36 Processing sheet with id= 69, first strand: chain 'p' and resid 29 through 33 removed outlier: 5.206A pdb=" N LEU p 81 " --> pdb=" O VAL p 98 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N HIS p 96 " --> pdb=" O ARG p 83 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'p' and resid 36 through 41 removed outlier: 5.169A pdb=" N LYS p 51 " --> pdb=" O ILE p 67 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N PHE p 61 " --> pdb=" O LEU p 57 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 't' and resid 4 through 10 removed outlier: 4.156A pdb=" N PHE t 16 " --> pdb=" O HIS t 9 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY t 37 " --> pdb=" O VAL t 19 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLY t 49 " --> pdb=" O ASN t 40 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'u' and resid 7 through 11 removed outlier: 7.245A pdb=" N GLU u 60 " --> pdb=" O VAL u 76 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER u 72 " --> pdb=" O CYS u 64 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'u' and resid 19 through 30 No H-bonds generated for sheet with id= 73 Processing sheet with id= 74, first strand: chain 'w' and resid 30 through 33 removed outlier: 4.455A pdb=" N LEU w 47 " --> pdb=" O VAL w 62 " (cutoff:3.500A) 1939 hydrogen bonds defined for protein. 5730 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3960 hydrogen bonds 6226 hydrogen bond angles 0 basepair planarities 1573 basepair parallelities 2645 stacking parallelities Total time for adding SS restraints: 257.98 Time building geometry restraints manager: 63.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.19: 28 1.19 - 1.35: 37703 1.35 - 1.50: 78063 1.50 - 1.66: 41256 1.66 - 1.81: 269 Bond restraints: 157319 Sorted by residual: bond pdb=" C5 5MU z 66 " pdb=" C6 5MU z 66 " ideal model delta sigma weight residual 1.155 1.438 -0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.155 1.433 -0.278 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.433 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.593 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.595 0.207 2.00e-02 2.50e+03 1.07e+02 ... (remaining 157314 not shown) Histogram of bond angle deviations from ideal: 45.73 - 66.04: 4 66.04 - 86.34: 6 86.34 - 106.65: 28393 106.65 - 126.96: 195043 126.96 - 147.26: 11992 Bond angle restraints: 235438 Sorted by residual: angle pdb=" OP1 U z 67 " pdb=" P U z 67 " pdb=" OP3 U z 67 " ideal model delta sigma weight residual 109.47 45.73 63.74 3.00e+00 1.11e-01 4.51e+02 angle pdb=" OP1 U z 8 " pdb=" P U z 8 " pdb=" OP3 U z 8 " ideal model delta sigma weight residual 109.47 46.09 63.38 3.00e+00 1.11e-01 4.46e+02 angle pdb=" O6 OMG z 17 " pdb=" C6 OMG z 17 " pdb=" N1 OMG z 17 " ideal model delta sigma weight residual 119.94 62.83 57.11 3.00e+00 1.11e-01 3.62e+02 angle pdb=" C5 OMG z 17 " pdb=" C6 OMG z 17 " pdb=" O6 OMG z 17 " ideal model delta sigma weight residual 120.11 63.64 56.47 3.00e+00 1.11e-01 3.54e+02 angle pdb=" OP2 G z 9 " pdb=" P G z 9 " pdb=" OP3 G z 9 " ideal model delta sigma weight residual 109.47 69.88 39.59 3.00e+00 1.11e-01 1.74e+02 ... (remaining 235433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 80904 35.92 - 71.84: 2690 71.84 - 107.75: 227 107.75 - 143.67: 15 143.67 - 179.59: 43 Dihedral angle restraints: 83879 sinusoidal: 67549 harmonic: 16330 Sorted by residual: dihedral pdb=" C4' C 12146 " pdb=" C3' C 12146 " pdb=" C2' C 12146 " pdb=" C1' C 12146 " ideal model delta sinusoidal sigma weight residual -35.00 33.38 -68.38 1 8.00e+00 1.56e-02 9.47e+01 dihedral pdb=" C5' C 12146 " pdb=" C4' C 12146 " pdb=" C3' C 12146 " pdb=" O3' C 12146 " ideal model delta sinusoidal sigma weight residual 147.00 79.34 67.66 1 8.00e+00 1.56e-02 9.30e+01 dihedral pdb=" O4' U z 59 " pdb=" C1' U z 59 " pdb=" N1 U z 59 " pdb=" C2 U z 59 " ideal model delta sinusoidal sigma weight residual -160.00 14.89 -174.89 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 83876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.413: 29990 0.413 - 0.827: 3 0.827 - 1.240: 0 1.240 - 1.654: 0 1.654 - 2.067: 1 Chirality restraints: 29994 Sorted by residual: chirality pdb=" P U z 20 " pdb=" OP1 U z 20 " pdb=" OP2 U z 20 " pdb=" O5' U z 20 " both_signs ideal model delta sigma weight residual True 2.41 -0.34 2.07 2.00e-01 2.50e+01 1.07e+02 chirality pdb=" C1* PSU 12580 " pdb=" O4* PSU 12580 " pdb=" C2* PSU 12580 " pdb=" C5 PSU 12580 " both_signs ideal model delta sigma weight residual False 2.55 1.76 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" C1* PSU 12457 " pdb=" O4* PSU 12457 " pdb=" C2* PSU 12457 " pdb=" C5 PSU 12457 " both_signs ideal model delta sigma weight residual False 2.55 2.00 0.55 2.00e-01 2.50e+01 7.47e+00 ... (remaining 29991 not shown) Planarity restraints: 12546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU z 66 " 0.092 2.00e-02 2.50e+03 6.50e-01 9.52e+03 pdb=" C4' 5MU z 66 " 0.482 2.00e-02 2.50e+03 pdb=" O4' 5MU z 66 " 0.781 2.00e-02 2.50e+03 pdb=" C3' 5MU z 66 " -0.593 2.00e-02 2.50e+03 pdb=" O3' 5MU z 66 " -0.683 2.00e-02 2.50e+03 pdb=" C2' 5MU z 66 " -0.186 2.00e-02 2.50e+03 pdb=" O2' 5MU z 66 " 0.989 2.00e-02 2.50e+03 pdb=" C1' 5MU z 66 " 0.165 2.00e-02 2.50e+03 pdb=" N1 5MU z 66 " -1.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " -0.081 2.00e-02 2.50e+03 6.35e-01 9.08e+03 pdb=" C4' 2MG 21516 " -0.470 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " -0.726 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " 0.679 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " 0.175 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " -0.993 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " -0.183 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " 1.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG z 17 " 0.930 2.00e-02 2.50e+03 6.16e-01 8.53e+03 pdb=" C4' OMG z 17 " -0.212 2.00e-02 2.50e+03 pdb=" O4' OMG z 17 " -0.665 2.00e-02 2.50e+03 pdb=" C3' OMG z 17 " 0.167 2.00e-02 2.50e+03 pdb=" O3' OMG z 17 " -0.992 2.00e-02 2.50e+03 pdb=" C2' OMG z 17 " 0.611 2.00e-02 2.50e+03 pdb=" O2' OMG z 17 " 0.682 2.00e-02 2.50e+03 pdb=" C1' OMG z 17 " -0.452 2.00e-02 2.50e+03 pdb=" N9 OMG z 17 " -0.069 2.00e-02 2.50e+03 ... (remaining 12543 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 698 2.31 - 2.96: 64860 2.96 - 3.61: 241889 3.61 - 4.25: 453224 4.25 - 4.90: 596491 Nonbonded interactions: 1357162 Sorted by model distance: nonbonded pdb=" O6 OMG z 17 " pdb=" C2 OMG z 17 " model vdw 1.667 2.608 nonbonded pdb=" OP1 C 1 948 " pdb="MG MG 13023 " model vdw 1.724 2.170 nonbonded pdb=" O6 OMG z 17 " pdb=" C4 OMG z 17 " model vdw 1.730 2.608 nonbonded pdb=" OP2 G 11430 " pdb="MG MG 13250 " model vdw 1.739 2.170 nonbonded pdb=" OP2 U 1 963 " pdb="MG MG 13023 " model vdw 1.751 2.170 ... (remaining 1357157 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 21.970 Check model and map are aligned: 1.580 Set scattering table: 0.920 Process input model: 540.180 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 573.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.283 157319 Z= 0.635 Angle : 0.969 63.740 235438 Z= 0.508 Chirality : 0.058 2.067 29994 Planarity : 0.021 0.650 12546 Dihedral : 14.308 179.588 73347 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.57 % Favored : 96.27 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.09), residues: 5634 helix: -3.59 (0.06), residues: 1917 sheet: -1.93 (0.14), residues: 1163 loop : -1.81 (0.10), residues: 2554 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1897 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1874 time to evaluate : 6.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 4 residues processed: 1889 average time/residue: 1.3307 time to fit residues: 4292.0288 Evaluate side-chains 1403 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1399 time to evaluate : 6.103 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 1.3870 time to fit residues: 15.7170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 855 optimal weight: 5.9990 chunk 767 optimal weight: 9.9990 chunk 426 optimal weight: 10.0000 chunk 262 optimal weight: 8.9990 chunk 517 optimal weight: 7.9990 chunk 410 optimal weight: 9.9990 chunk 793 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 chunk 482 optimal weight: 5.9990 chunk 590 optimal weight: 5.9990 chunk 919 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN D 136 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN H 2 GLN H 18 GLN H 128 HIS I 67 ASN J 5 GLN J 9 ASN J 29 HIS M 18 GLN N 38 GLN O 12 GLN P 20 GLN P 56 GLN Q 18 GLN Q 82 HIS R 40 ASN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 ASN X 15 ASN X 36 GLN X 58 ASN Y 9 GLN c 6 GLN d 31 HIS ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 51 ASN f 170 HIS h 36 GLN h 140 ASN k 97 ASN m 4 ASN m 126 GLN n 56 HIS o 28 ASN p 6 GLN p 77 HIS p 112 GLN q 14 HIS r 49 GLN r 66 GLN u 51 ASN ** v 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 HIS ** B 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.174 157319 Z= 0.325 Angle : 0.717 58.112 235438 Z= 0.369 Chirality : 0.038 1.213 29994 Planarity : 0.007 0.132 12546 Dihedral : 14.452 179.023 62057 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.09 % Favored : 96.88 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.10), residues: 5634 helix: -0.37 (0.11), residues: 1935 sheet: -1.22 (0.15), residues: 1083 loop : -1.21 (0.11), residues: 2616 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1758 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1618 time to evaluate : 6.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 140 outliers final: 88 residues processed: 1660 average time/residue: 1.3379 time to fit residues: 3869.4299 Evaluate side-chains 1524 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1436 time to evaluate : 6.010 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 0 residues processed: 88 average time/residue: 1.1143 time to fit residues: 193.7284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 511 optimal weight: 20.0000 chunk 285 optimal weight: 10.0000 chunk 765 optimal weight: 8.9990 chunk 626 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 chunk 921 optimal weight: 20.0000 chunk 995 optimal weight: 5.9990 chunk 820 optimal weight: 9.9990 chunk 913 optimal weight: 6.9990 chunk 314 optimal weight: 10.0000 chunk 739 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 HIS I 67 ASN J 3 GLN J 5 GLN J 29 HIS J 89 ASN J 93 GLN N 98 GLN P 56 GLN R 40 ASN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 17 ASN X 36 GLN X 45 GLN Z 41 HIS ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 41 GLN ** i 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 21 ASN m 50 GLN ** o 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 112 GLN ** r 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 66 GLN u 51 ASN ** v 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 78 ASN x 84 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.179 157319 Z= 0.358 Angle : 0.697 59.930 235438 Z= 0.360 Chirality : 0.038 1.169 29994 Planarity : 0.006 0.134 12546 Dihedral : 14.417 179.294 62057 Min Nonbonded Distance : 1.000 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.11), residues: 5634 helix: 0.68 (0.12), residues: 1948 sheet: -0.99 (0.15), residues: 1090 loop : -0.99 (0.12), residues: 2596 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1661 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1545 time to evaluate : 8.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 61 residues processed: 1589 average time/residue: 1.3532 time to fit residues: 3779.5008 Evaluate side-chains 1488 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1427 time to evaluate : 6.109 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 1.2127 time to fit residues: 143.2553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 910 optimal weight: 9.9990 chunk 692 optimal weight: 7.9990 chunk 478 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 439 optimal weight: 10.0000 chunk 618 optimal weight: 6.9990 chunk 924 optimal weight: 6.9990 chunk 979 optimal weight: 10.0000 chunk 483 optimal weight: 4.9990 chunk 876 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 226 ASN D 136 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN J 3 GLN J 5 GLN J 29 HIS J 89 ASN O 56 HIS P 44 GLN P 56 GLN R 40 ASN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 17 ASN X 36 GLN X 45 GLN e 35 GLN g 41 GLN h 36 GLN h 136 GLN h 140 ASN ** i 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 21 ASN m 50 GLN ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 112 GLN r 49 GLN r 66 GLN t 29 ASN ** t 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 48 GLN x 84 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.179 157319 Z= 0.304 Angle : 0.676 59.929 235438 Z= 0.349 Chirality : 0.037 1.170 29994 Planarity : 0.006 0.129 12546 Dihedral : 14.414 179.531 62057 Min Nonbonded Distance : 1.021 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.11), residues: 5634 helix: 0.95 (0.12), residues: 1960 sheet: -0.82 (0.15), residues: 1111 loop : -0.89 (0.12), residues: 2563 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1634 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1530 time to evaluate : 6.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 53 residues processed: 1562 average time/residue: 1.2973 time to fit residues: 3553.0928 Evaluate side-chains 1473 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1420 time to evaluate : 6.112 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 1.0428 time to fit residues: 112.7182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 815 optimal weight: 10.0000 chunk 555 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 729 optimal weight: 9.9990 chunk 404 optimal weight: 20.0000 chunk 835 optimal weight: 20.0000 chunk 676 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 499 optimal weight: 6.9990 chunk 878 optimal weight: 20.0000 chunk 247 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 5 GLN J 29 HIS J 89 ASN P 44 GLN P 56 GLN R 40 ASN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 17 ASN X 36 GLN X 45 GLN g 190 HIS h 126 ASN h 136 GLN ** i 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 3 HIS ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 21 ASN ** m 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN o 101 ASN p 112 GLN ** r 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 66 GLN ** t 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN w 14 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.179 157319 Z= 0.339 Angle : 0.688 59.976 235438 Z= 0.355 Chirality : 0.037 1.168 29994 Planarity : 0.006 0.131 12546 Dihedral : 14.410 179.829 62057 Min Nonbonded Distance : 1.023 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.11), residues: 5634 helix: 1.04 (0.12), residues: 1954 sheet: -0.74 (0.15), residues: 1123 loop : -0.80 (0.12), residues: 2557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1566 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1478 time to evaluate : 6.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 46 residues processed: 1506 average time/residue: 1.2581 time to fit residues: 3327.8054 Evaluate side-chains 1465 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1419 time to evaluate : 6.150 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 1.0197 time to fit residues: 96.8937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 329 optimal weight: 10.0000 chunk 881 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 574 optimal weight: 8.9990 chunk 241 optimal weight: 10.0000 chunk 980 optimal weight: 8.9990 chunk 813 optimal weight: 20.0000 chunk 453 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 514 optimal weight: 5.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 104 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 5 GLN J 29 HIS J 89 ASN ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 56 GLN Q 43 ASN R 40 ASN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 17 ASN X 45 GLN Z 65 ASN f 122 GLN h 36 GLN h 136 GLN ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 21 ASN ** m 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN ** n 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 112 GLN r 43 ASN ** r 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 66 GLN s 20 ASN ** t 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN x 48 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.179 157319 Z= 0.363 Angle : 0.699 59.993 235438 Z= 0.360 Chirality : 0.038 1.168 29994 Planarity : 0.006 0.131 12546 Dihedral : 14.431 179.998 62057 Min Nonbonded Distance : 1.012 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.11), residues: 5634 helix: 1.03 (0.12), residues: 1950 sheet: -0.66 (0.15), residues: 1106 loop : -0.75 (0.12), residues: 2578 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1559 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1462 time to evaluate : 8.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 63 residues processed: 1493 average time/residue: 1.2883 time to fit residues: 3386.9211 Evaluate side-chains 1468 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1405 time to evaluate : 6.016 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 1.0328 time to fit residues: 130.2092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 944 optimal weight: 1.9990 chunk 110 optimal weight: 40.0000 chunk 558 optimal weight: 6.9990 chunk 715 optimal weight: 20.0000 chunk 554 optimal weight: 8.9990 chunk 825 optimal weight: 7.9990 chunk 547 optimal weight: 10.0000 chunk 976 optimal weight: 2.9990 chunk 611 optimal weight: 10.0000 chunk 595 optimal weight: 0.0270 chunk 450 optimal weight: 10.0000 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 5 GLN J 29 HIS J 89 ASN J 93 GLN P 56 GLN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 ASN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 45 GLN Z 65 ASN d 28 ASN h 36 GLN l 4 GLN l 16 ASN ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 21 ASN ** m 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN ** n 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 112 GLN ** r 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 20 ASN ** t 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.179 157319 Z= 0.212 Angle : 0.664 59.612 235438 Z= 0.344 Chirality : 0.035 1.155 29994 Planarity : 0.006 0.125 12546 Dihedral : 14.394 179.960 62057 Min Nonbonded Distance : 1.062 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.11), residues: 5634 helix: 1.06 (0.12), residues: 1963 sheet: -0.50 (0.16), residues: 1098 loop : -0.72 (0.12), residues: 2573 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1498 time to evaluate : 6.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 28 residues processed: 1516 average time/residue: 1.3131 time to fit residues: 3500.8579 Evaluate side-chains 1456 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1428 time to evaluate : 6.037 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 1.0644 time to fit residues: 63.8630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 604 optimal weight: 0.0020 chunk 389 optimal weight: 20.0000 chunk 583 optimal weight: 6.9990 chunk 294 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 620 optimal weight: 9.9990 chunk 665 optimal weight: 8.9990 chunk 482 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 767 optimal weight: 9.9990 overall best weight: 6.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 5 GLN J 29 HIS J 89 ASN P 44 GLN P 56 GLN P 59 GLN R 40 ASN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 ASN c 29 GLN d 28 ASN g 190 HIS h 36 GLN l 4 GLN ** l 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 21 ASN ** m 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 5 ASN p 112 GLN ** r 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN w 69 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.179 157319 Z= 0.311 Angle : 0.689 59.681 235438 Z= 0.355 Chirality : 0.037 1.161 29994 Planarity : 0.006 0.130 12546 Dihedral : 14.375 179.964 62057 Min Nonbonded Distance : 1.031 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.11), residues: 5634 helix: 1.07 (0.12), residues: 1949 sheet: -0.50 (0.16), residues: 1111 loop : -0.71 (0.12), residues: 2574 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1484 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1431 time to evaluate : 6.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 38 residues processed: 1440 average time/residue: 1.3106 time to fit residues: 3310.4563 Evaluate side-chains 1438 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1400 time to evaluate : 6.127 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 1.0824 time to fit residues: 85.2896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 888 optimal weight: 6.9990 chunk 935 optimal weight: 9.9990 chunk 853 optimal weight: 5.9990 chunk 909 optimal weight: 9.9990 chunk 547 optimal weight: 20.0000 chunk 396 optimal weight: 10.0000 chunk 714 optimal weight: 9.9990 chunk 279 optimal weight: 20.0000 chunk 822 optimal weight: 6.9990 chunk 860 optimal weight: 6.9990 chunk 906 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN J 29 HIS J 89 ASN M 9 GLN P 56 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 ASN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 ASN d 28 ASN h 36 GLN ** j 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 4 GLN ** l 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 21 ASN ** m 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 112 GLN ** r 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 20 ASN ** t 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.179 157319 Z= 0.340 Angle : 0.703 59.840 235438 Z= 0.363 Chirality : 0.037 1.163 29994 Planarity : 0.006 0.168 12546 Dihedral : 14.397 179.772 62057 Min Nonbonded Distance : 1.018 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.11), residues: 5634 helix: 1.00 (0.12), residues: 1947 sheet: -0.47 (0.16), residues: 1105 loop : -0.71 (0.12), residues: 2582 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1472 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1438 time to evaluate : 6.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 25 residues processed: 1445 average time/residue: 1.3055 time to fit residues: 3307.0041 Evaluate side-chains 1428 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1403 time to evaluate : 6.063 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 1.0098 time to fit residues: 54.0325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 597 optimal weight: 0.9980 chunk 962 optimal weight: 1.9990 chunk 587 optimal weight: 0.7980 chunk 456 optimal weight: 6.9990 chunk 668 optimal weight: 0.9980 chunk 1009 optimal weight: 1.9990 chunk 928 optimal weight: 9.9990 chunk 803 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 620 optimal weight: 5.9990 chunk 492 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN J 29 HIS J 89 ASN P 56 GLN R 40 ASN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 ASN h 36 GLN h 136 GLN ** j 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 21 ASN ** n 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 112 GLN q 14 HIS r 43 ASN ** r 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 20 ASN t 26 ASN ** t 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 9 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.179 157319 Z= 0.148 Angle : 0.679 59.223 235438 Z= 0.349 Chirality : 0.033 1.142 29994 Planarity : 0.006 0.121 12546 Dihedral : 14.350 179.674 62057 Min Nonbonded Distance : 1.202 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.41 % Favored : 96.57 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 5634 helix: 1.04 (0.12), residues: 1920 sheet: -0.31 (0.16), residues: 1082 loop : -0.67 (0.12), residues: 2632 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1507 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1486 time to evaluate : 5.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 1491 average time/residue: 1.2486 time to fit residues: 3257.5415 Evaluate side-chains 1436 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1423 time to evaluate : 6.071 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 1.0532 time to fit residues: 32.4601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 638 optimal weight: 4.9990 chunk 856 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 740 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 804 optimal weight: 0.5980 chunk 336 optimal weight: 30.0000 chunk 826 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 29 HIS J 89 ASN J 93 GLN P 20 GLN P 56 GLN P 59 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 ASN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 36 GLN h 136 GLN ** j 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 21 ASN m 25 ASN ** n 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 118 HIS ** r 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.043099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.033726 restraints weight = 841382.879| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 1.71 r_work: 0.2519 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2421 r_free = 0.2421 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2421 r_free = 0.2421 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.179 157319 Z= 0.268 Angle : 0.685 59.455 235438 Z= 0.353 Chirality : 0.036 1.157 29994 Planarity : 0.006 0.128 12546 Dihedral : 14.269 179.969 62057 Min Nonbonded Distance : 1.031 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.55 % Favored : 96.43 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.11), residues: 5634 helix: 0.98 (0.12), residues: 1939 sheet: -0.31 (0.16), residues: 1089 loop : -0.67 (0.12), residues: 2606 =============================================================================== Job complete usr+sys time: 49001.61 seconds wall clock time: 850 minutes 31.73 seconds (51031.73 seconds total)